What is the grammar rule for the preposition after the word free? Why do we say free of impurities but free of charge?
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The "charge" vs. "impurities" difference you actually seem to be asking about is nothing to do with the preposition as such; it's to do with "charge" being a "mass noun", so not calling for pluralization, and "impurity" being a "count noun", which it's appropriate to pluralize here.
This distinction is the same one as produces the "less vs. fewer" dichotomy.
There are other prepositions you could use with "free" as well:
I could go on ...